ProjectRNAseqCelegans/Week 9-10 code at main · olinm/ProjectRNAseqCelegans · GitHub

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#WEEK 9-10

---
TITLE: "Oliwia's RNASeq notebook: part 6"
---

Gene ontology

---
RStudio info
---
platform       x86_64-w64-mingw32
arch           x86_64
os             mingw32
system         x86_64, mingw32
status
major          4
minor          1.3
year           2022
month          03
day            10
svn rev        81868
language       R
version.string R version 4.1.3 (2022-03-10)
nickname       One Push-Up

---
 PART 1: RNASEQ GENE SET TESTING
---
References:
https://sbc.shef.ac.uk/workshops/2020-02-13-rnaseq-r/rna-seq-gene-set-testing.nb.html
https://bioinformatics-core-shared-training.github.io/RNAseq-R/rna-seq-gene-set-testing.nb.html
https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html#Plots_after_testing_for_DE

Gene ontology (GO) testing with goana

#installing the package
```{r}
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("limma")

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("org.Ce.eg.db")

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GO.db")

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

BiocManager::install("topGO")
```

#attach
```{r}
library(limma)
library(org.Ce.eg.db)
library(GO.db)
library(topGO)
```
#adding ENTREZID annotation to the table
```{r}
res2$ENTREZID = mapIds(org.Ce.eg.db,
                       key=res2$sequence_name,
                       column="ENTREZID",
                       keytype="WORMBASE",
                       multiVals="first")
```
#separation of + and - log2 fold change genes
```{r}
res2 <- mutate(res2, updown=ifelse(res2$log2FoldChange>0, "up", "down"))
res3 <- subset(res2, updown!="down" )
res3 = na.omit(res3)

res4 <- subset(res2, updown!="up" )
res4 = na.omit(res4)
```

#fixing the GO test to show up and down regulation
```{r}
IDs<-res2$ENTREZID

go <- goana(list(Up=res3$ENTREZID, Down=res4$ENTREZID), species="Ce")

topGO(go, n=10)
```

#different package could be explored for more possibilities with graphs

---
SESSION INFO
---

R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_Europe.1252  LC_CTYPE=English_Europe.1252    LC_MONETARY=English_Europe.1252
[4] LC_NUMERIC=C                    LC_TIME=English_Europe.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.6.0        Biobase_2.54.0              httr_1.4.2
 [4] bit64_4.0.5                 splines_4.1.3               assertthat_0.2.1
 [7] BiocManager_1.30.16         stats4_4.1.3                blob_1.2.2
[10] GenomeInfoDbData_1.2.7      yaml_2.3.5                  pillar_1.7.0
[13] RSQLite_2.2.10              lattice_0.20-45             glue_1.6.1
[16] digest_0.6.29               GenomicRanges_1.46.1        RColorBrewer_1.1-2
[19] XVector_0.34.0              colorspace_2.0-3            htmltools_0.5.2
[22] Matrix_1.4-0                DESeq2_1.34.0               XML_3.99-0.8
[25] pkgconfig_2.0.3             genefilter_1.76.0           zlibbioc_1.40.0
[28] purrr_0.3.4                 xtable_1.8-4                scales_1.1.1
[31] tzdb_0.2.0                  BiocParallel_1.28.3         tibble_3.1.6
[34] annotate_1.72.0             KEGGREST_1.34.0             generics_0.1.2
[37] IRanges_2.28.0              ggplot2_3.3.5               ellipsis_0.3.2
[40] cachem_1.0.6                SummarizedExperiment_1.24.0 BiocGenerics_0.40.0
[43] cli_3.2.0                   survival_3.2-13             magrittr_2.0.2
[46] crayon_1.5.0                memoise_2.0.1               evaluate_0.15
[49] fansi_1.0.2                 tools_4.1.3                 hms_1.1.1
[52] lifecycle_1.0.1             matrixStats_0.61.0          S4Vectors_0.32.3
[55] munsell_0.5.0               locfit_1.5-9.4              DelayedArray_0.20.0
[58] AnnotationDbi_1.56.2        Biostrings_2.62.0           compiler_4.1.3
[61] GenomeInfoDb_1.30.1         rlang_1.0.1                 grid_4.1.3
[64] RCurl_1.98-1.6              rstudioapi_0.13             bitops_1.0-7
[67] rmarkdown_2.13              gtable_0.3.0                DBI_1.1.2
[70] R6_2.5.1                    knitr_1.37                  dplyr_1.0.8
[73] fastmap_1.1.0               bit_4.0.4                   utf8_1.2.2
[76] readr_2.1.2                 parallel_4.1.3              Rcpp_1.0.8
[79] vctrs_0.3.8                 geneplotter_1.72.0          png_0.1-7
[82] tidyselect_1.1.2            xfun_0.29